Summary

cBioPortal provides a robust platform for visualizing, analyzing, and downloading large-scale cancer genomics datasets. It serves researchers and power users by offering tools to explore complex genomic information, facilitating discoveries in cancer research. The platform's architecture is evolving, with a significant database backend shift in its latest development version.

How It Works

The project's core architecture is undergoing a major transition. Version 7 (currently on the master branch) exclusively utilizes ClickHouse as its database backend, a departure from the traditional MySQL database used in previous versions (v6). This shift aims to leverage ClickHouse's capabilities for handling large-scale genomic data analysis. The portal is designed modularly, with distinct repositories for frontend and backend components, allowing for focused development.

Quick Start & Requirements

Local development and deployment are primarily facilitated via Docker Compose. The recommended approach involves building a custom Docker image and integrating it into the cbioportal-docker-compose setup. For end-to-end testing, Node.js (v18+) is a prerequisite. Detailed setup and architecture documentation are available online.

• Primary run command: docker compose up (after image configuration).
• Prerequisites: Docker, Node.js (v18+ for E2E tests), ClickHouse (for v7) or MySQL (for v6).
• Documentation: https://docs.cbioportal.org
• Community: https://slack.cbioportal.org

Highlighted Details

• Version 7 introduces a ClickHouse-only database backend, marking a significant architectural change incompatible with prior MySQL deployments.
• A dedicated maintenance-v6 branch exists for users still running v6, receiving only critical security updates.
• The project employs a layered testing strategy: Unit, Integration, and End-to-End (E2E) tests, with E2E tests written in JavaScript/TypeScript using Mocha and Chai.

Maintenance & Community

The project is actively preparing for v7, with the master branch serving as the pre-release branch. A dedicated maintenance-v6 branch ensures support for existing v6 deployments, focusing solely on security fixes. Community interaction and development coordination are primarily handled via Slack (https://slack.cbioportal.org) and email (cbioportal@cbioportal.org).

Licensing & Compatibility

The project's license details are available in the LICENSE file. A critical compatibility note is that the v7 database setup (ClickHouse-only) is not compatible with earlier portal settings or the traditional MySQL mode.

Limitations & Caveats

The v7 database architecture, exclusively using ClickHouse, is incompatible with previous MySQL configurations and existing study importer tools. The master branch is designated as a pre-release branch for v7. Version 6 is in a maintenance-only state, receiving only security patches.